de.jstacs.algorithms
Class Alignment.SimpleCosts

java.lang.Object
  extended by de.jstacs.algorithms.Alignment.SimpleCosts
All Implemented Interfaces:
Alignment.Costs
Enclosing class:
Alignment

public static class Alignment.SimpleCosts
extends Object
implements Alignment.Costs

Class for simple costs with costs mismatch for a mismatch, costs start to start a new gap, costs elong to elongate a gap by one position and costs of 0 for a match.


Nested Class Summary
 
Nested classes/interfaces inherited from interface de.jstacs.algorithms.Alignment.Costs
Alignment.Costs.Direction
 
Constructor Summary
Alignment.SimpleCosts(double mismatch, double start, double elong)
          Creates a new instance of simple costs with costs mismatch for a mismatch, costs start to start a new gap, costs elong to elongate a gap by one position and costs of 0 for a match.
 
Method Summary
 double getCostFor(Sequence s1, Sequence s2, int i, int j, Alignment.Costs.Direction from)
          Returns the costs for the alignment if s1(i) and s2(j) coming from from.
 double getElongateCosts()
          Returns the costs to elongate a gap by one position.
 double getGapCostsFor(int length)
          Returns the costs for a gap of length length.
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

Alignment.SimpleCosts

public Alignment.SimpleCosts(double mismatch,
                             double start,
                             double elong)
Creates a new instance of simple costs with costs mismatch for a mismatch, costs start to start a new gap, costs elong to elongate a gap by one position and costs of 0 for a match.

Parameters:
mismatch - the mismatch costs
start - the costs to start a gap
elong - the costs to elongate a gap
Method Detail

getCostFor

public double getCostFor(Sequence s1,
                         Sequence s2,
                         int i,
                         int j,
                         Alignment.Costs.Direction from)
Description copied from interface: Alignment.Costs
Returns the costs for the alignment if s1(i) and s2(j) coming from from.

Specified by:
getCostFor in interface Alignment.Costs
Parameters:
s1 - the first sequence
s2 - the second sequence
i - the index in the first sequence
j - the index in the second sequence
from - the direction within the DP-matrix
Returns:
the costs

getElongateCosts

public double getElongateCosts()
Description copied from interface: Alignment.Costs
Returns the costs to elongate a gap by one position.

Specified by:
getElongateCosts in interface Alignment.Costs
Returns:
the corresponding costs

getGapCostsFor

public double getGapCostsFor(int length)
Description copied from interface: Alignment.Costs
Returns the costs for a gap of length length.

Specified by:
getGapCostsFor in interface Alignment.Costs
Parameters:
length - the length of the gap
Returns:
the corresponding costs